chr6-52452780-GTATGTCAC-AAG

Variant names:

• chr6-52452780-GTATGTCAC-AAG
• rs1554259746
• NM_018100.4:c.666_674delGTATGTCACinsAAG

Variant summary

Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PM2 PM4

The NM_018100.4(EFHC1):​c.666_674delGTATGTCACinsAAG​(p.Tyr223_Thr225delinsSer) variant causes a missense, disruptive inframe deletion change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: EFHC1 NM_018100.4 missense, disruptive_inframe_deletion
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.47
• Publications: 0 publications found

Genes affected

EFHC1 (HGNC:16406): (EF-hand domain containing 1) This gene encodes an EF-hand-containing calcium binding protein. The encoded protein likely plays a role in calcium homeostasis. Mutations in this gene have been associated with susceptibility to juvenile myoclonic epilepsy and juvenile absence epilepsy. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2010]

EFHC1 Gene-Disease associations (from GenCC):

• juvenile myoclonic epilepsy

  Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
• epilepsy

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Uncertain_significance. The variant received 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_018100.4.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018100.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFHC1	NM_018100.4	MANE Select	c.666_674delGTATGTCACinsAAG	p.Tyr223_Thr225delinsSer	missense disruptive_inframe_deletion	N/A	NP_060570.2
	EFHC1	NM_001172420.2		c.609_617delGTATGTCACinsAAG	p.Tyr204_Thr206delinsSer	missense disruptive_inframe_deletion	N/A	NP_001165891.1
	EFHC1	NR_033327.2		n.735_743delGTATGTCACinsAAG		non_coding_transcript_exon	Exon 4 of 10

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFHC1	ENST00000371068.11	TSL:1 MANE Select	c.666_674delGTATGTCACinsAAG	p.Tyr223_Thr225delinsSer	missense disruptive_inframe_deletion	N/A	ENSP00000360107.4
	EFHC1	ENST00000637340.1	TSL:1	n.1334_1342delGTATGTCACinsAAG		non_coding_transcript_exon	Exon 4 of 10
	EFHC1	ENST00000637353.1	TSL:5	c.666_674delGTATGTCACinsAAG	p.Tyr223_Thr225delinsSer	missense disruptive_inframe_deletion	N/A	ENSP00000490441.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions as Germline

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	Myoclonic epilepsy, juvenile, susceptibility to, 1;C5551411:Typical absence seizure (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		4.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1554259746; hg19: chr6-52317578;